Re: Problem with "CH2" atom -- January 11, 2011 - 10:04

Ok, this should now be fixed.  If you have any other atom names that
could be included, that would be quite useful.  If you like and have
the time, maybe you could even make the changes yourself on an SVN
copy of relax and send the patch file ($ svn diff > patch) to be
applied to the 1.3 main line.

Cheers,

Edward


On 19 December 2010 05:20, V.V. <vvostri@xxxxxxxxx> wrote:
> Edward,
>
> It looks like the digits are stripped from the element name in
> generic_fns/structure/internal.py, so it should be 'CH' and not 'CH2'
> in the table. Could you please update the file?
>
> Thank you,
> Vitaly
>
>
> On Fri, Dec 17, 2010 at 13:08, V.V. <vvostri@xxxxxxxxx> wrote:
> > Thank you very much, Edward!
> >
> > Vitaly
> >
> >
> > On Fri, Dec 17, 2010 at 13:03, Edward d'Auvergne <edward@xxxxxxxxxxxxx> 
> > wrote:
> > > Thank you for the detailed message and creating the bug report.  This
> > > is now fixed.  Cheers.  If you would like the changes without waiting
> > > for a new release of relax, the new code can be checked out from the
> > > repository by typing:
> > >
> > > $ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3
> > >
> > > or if this doesn't work:
> > >
> > > $ svn co http://svn.gna.org/svn/relax/1.3 relax-1.3
> > >
> > > If you already have a checked out copy, try typing:
> > >
> > > $ svn up
> > >
> > > This requires installation of the subversion program
> > > (http://subversion.tigris.org/).
> > >
> > > Regards,
> > >
> > > Edward
> > >
> > >
> > > On 17 December 2010 19:52, V.V. <vvostri@xxxxxxxxx> wrote:
> > > > Thank you, Edward!
> > > > I have submitted the bug report (#17343). Yes, the atom name in the
> > > > pdb file is labeled "CH2".
> > > >
> > > > Vitaly
> > > >
> > > >
> > > >
> > > > On Fri, Dec 17, 2010 at 11:38, Edward d'Auvergne <edward@xxxxxxxxxxxxx> 
> > > > wrote:
> > > > > Hi Vitaly,
> > > > >
> > > > > Thank you for identifying this problem.  I just had a question, is the
> > > > > atom named 'CH2' within the PDB file?  If you don't mind, would you be
> > > > > able to create a bug report for this?  This would be much appreciated
> > > > > as it would help other relax users who encounter the same problem as
> > > > > you have found.  This is not too important as it is a missing feature
> > > > > rather than a bug but, if you could, the bug report submission page is
> > > > > https://gna.org/bugs/?func=additem&group=relax.
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > >
> > > > > On 15 December 2010 02:51, V.V. <vvostri@xxxxxxxxx> wrote:
> > > > > > Hello,
> > > > > >
> > > > > > I am trying to create a diffusion tensor from the results file, and I
> > > > > > am running into a following problem after
> > > > > > "structure.create_diff_tensor_pdb" is invoked:
> > > > > >
> > > > > > ================
> > > > > > relax> structure.create_diff_tensor_pdb(scale=1.7999999999999999e-06,
> > > > > > file='tensor.pdb', dir=None, force=True)
> > > > > > Adding molecule 'diff_tensor' to model None (from the original
> > > > > > molecule number None of model None)
> > > > > >
> > > > > > Chain A
> > > > > >
> > > > > > Calculating the centre of mass.
> > > > > > RelaxWarning: Skipping the atom '#ave_mol1:2@30' as the element name
> > > > > > does not exist in the PDB file.
> > > > > > ================
> > > > > >
> > > > > > In the "results" file, element 30 in the atom name list is 'CH2' (Trp
> > > > > > side chain). Also if I read the structure file with
> > > > > > "structure.read_pdb", for each of the Trp residues I get:
> > > > > >
> > > > > > ================
> > > > > > RelaxWarning: Cannot determine the element associated with atom 'CH2'.
> > > > > > ================
> > > > > >
> > > > > > It looks like this atom was left out
> > > > > > (http://www.mail-archive.com/relax-commits@xxxxxxx/msg06219.html).
> > > > > > Also, if possible, could you append "OT" atom name (XPLOR format) to
> > > > > > the oxygen list?
> > > > > >
> > > > > > Thank you,
> > > > > > Vitaly
> > > > > >
> > > > > > _______________________________________________
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> > > > > >
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